Functional Groups

Functional Groups 180 groups, 48 parent groups

The ATB tags compounds with named functional groups, derived from the structure. Each group is a small query graph: a pattern of atoms and bonds with conditions on each atom, matched as a subgraph of the molecule’s own graph. One occurrence is one distinct set of the pattern’s anchor atoms, so a carboxylate’s two equivalent oxygens count once. A group is not counted where its atoms lie inside a match of a group that takes precedence over it (an ester’s O is not also an ether). Parent groups (amine, halogen, …) are never matched themselves: a compound has a parent group when it has any of the groups under it. In the drawings, a note beside a carbon says what the letter alone does not (sp3, sp2, aromatic, …): it is what tells the alkyl, vinyl and aryl forms of a group apart. Open a group to see exactly what it matches and what it does not.

Annotation scheme 2. Counts are of the annotated compounds (245,759): those with experimental reference data plus small, neutral organic compounds (up to 12 heavy atoms; carbon with H, N, O, S, P, F, Cl, Br, I), not of every ATB molecule. Counts as of 2026-10-21 05:31. The vocabulary is also available as JSON: GET /api/v1/functional_groups.

Carbon frameworks

alkene alkene
Query graph of alkene
69,045 compounds, 183 with experimental data
alkyne alkyne
Query graph of alkyne
24,200 compounds, 18 with experimental data
allene allene
Query graph of allene
36 compounds, 2 with experimental data
cyclopropane cyclopropane
Query graph of cyclopropane
31,352 compounds, 14 with experimental data
within: cycloalkane ring
cyclobutane cyclobutane
Query graph of cyclobutane
29,475 compounds, 11 with experimental data
within: cycloalkane ring
cyclopentane cyclopentane
Query graph of cyclopentane
9,597 compounds, 25 with experimental data
within: cycloalkane ring
cyclohexane cyclohexane
Query graph of cyclohexane
2,063 compounds, 56 with experimental data
within: cycloalkane ring
cycloheptane cycloheptane
Query graph of cycloheptane
140 compounds, 3 with experimental data
within: cycloalkane ring
cyclooctane cyclooctane
Query graph of cyclooctane
20 compounds, 2 with experimental data
within: cycloalkane ring

Halogens

fluoro (alkyl) fluoro_alkyl
Query graph of fluoro (alkyl)
1,861 compounds, 78 with experimental data
within: fluoro, alkyl halide
fluoro (aryl) fluoro_aryl
Query graph of fluoro (aryl)
2,216 compounds, 37 with experimental data
within: fluoro, aryl halide
fluoro (vinyl) fluoro_vinyl
Query graph of fluoro (vinyl)
478 compounds, 2 with experimental data
within: fluoro, vinyl halide
chloro (alkyl) chloro_alkyl
Query graph of chloro (alkyl)
2,411 compounds, 107 with experimental data
within: chloro, alkyl halide
chloro (aryl) chloro_aryl
Query graph of chloro (aryl)
1,869 compounds, 104 with experimental data
within: chloro, aryl halide
chloro (vinyl) chloro_vinyl
Query graph of chloro (vinyl)
2,345 compounds, 18 with experimental data
within: chloro, vinyl halide
bromo (alkyl) bromo_alkyl
Query graph of bromo (alkyl)
1,091 compounds, 53 with experimental data
within: bromo, alkyl halide
bromo (aryl) bromo_aryl
Query graph of bromo (aryl)
939 compounds, 27 with experimental data
within: bromo, aryl halide
bromo (vinyl) bromo_vinyl
Query graph of bromo (vinyl)
961 compounds
within: bromo, vinyl halide
iodo (alkyl) iodo_alkyl
Query graph of iodo (alkyl)
85 compounds, 11 with experimental data
within: iodo, alkyl halide
iodo (aryl) iodo_aryl
Query graph of iodo (aryl)
180 compounds, 11 with experimental data
within: iodo, aryl halide
iodo (vinyl) iodo_vinyl
Query graph of iodo (vinyl)
68 compounds
within: iodo, vinyl halide
halide ion halide_ion
Query graph of halide ion
3 compounds, 3 with experimental data

Oxygen: hydroxyl family

alcohol I alcohol_primary
Query graph of alcohol I
29,072 compounds, 132 with experimental data
within: alcohol
alcohol II alcohol_secondary
Query graph of alcohol II
21,839 compounds, 86 with experimental data
within: alcohol
alcohol III alcohol_tertiary
Query graph of alcohol III
11,138 compounds, 18 with experimental data
within: alcohol
alkoxide alkoxide
Query graph of alkoxide
15,108 compounds, 12 with experimental data
within: alcohol or alkoxide
phenol phenol
Query graph of phenol
7,483 compounds, 79 with experimental data
within: phenol or phenoxide
phenoxide phenoxide
Query graph of phenoxide
1,117 compounds, 23 with experimental data
within: phenol or phenoxide
enol enol
Query graph of enol
10,945 compounds
within: enol or enolate
enolate enolate
Query graph of enolate
8,197 compounds, 6 with experimental data
within: enol or enolate

Oxygen: ethers and acetals

ether (aliphatic) ether_aliphatic
Query graph of ether (aliphatic)
42,883 compounds, 134 with experimental data
within: ether
aryl ether ether_aryl
Query graph of aryl ether
2,984 compounds, 81 with experimental data
within: ether
epoxide epoxide
Query graph of epoxide
10,445 compounds, 19 with experimental data
within: ether
aziridine aziridine
Query graph of aziridine
19,036 compounds, 3 with experimental data
acetal acetal
Query graph of acetal
3,124 compounds, 27 with experimental data
within: acetal/ketal
ketal ketal
Query graph of ketal
294 compounds, 7 with experimental data
within: acetal/ketal
hemiacetal hemiacetal
Query graph of hemiacetal
1,333 compounds, 3 with experimental data
within: hemiacetal/hemiketal
hemiketal hemiketal
Query graph of hemiketal
31 compounds
within: hemiacetal/hemiketal
orthoester orthoester
Query graph of orthoester
11 compounds, 9 with experimental data
aminal / N,O- or S-acetal heteroacetal
Query graph of aminal / N,O- or S-acetal
22,681 compounds, 6 with experimental data
peroxide peroxide
Query graph of peroxide
125 compounds, 9 with experimental data

Oxygen: carbonyl family

aldehyde aldehyde
Query graph of aldehyde
15,945 compounds, 43 with experimental data
ketone ketone
Query graph of ketone
18,777 compounds, 98 with experimental data
carboxylic acid carboxylic_acid
Query graph of carboxylic acid
7,933 compounds, 43 with experimental data
within: carboxylic acid or carboxylate
carboxylate carboxylate
Query graph of carboxylate
4,717 compounds, 40 with experimental data
within: carboxylic acid or carboxylate
ester ester
Query graph of ester
3,943 compounds, 218 with experimental data
within: carboxylic ester (incl. lactone)
lactone lactone
Query graph of lactone
4,459 compounds, 27 with experimental data
within: carboxylic ester (incl. lactone)
anhydride anhydride
Query graph of anhydride
68 compounds, 6 with experimental data
acyl halide acyl_halide
Query graph of acyl halide
60 compounds, 2 with experimental data
carbonate carbonate
Query graph of carbonate
215 compounds, 11 with experimental data
protonated carbonyl carbonyl_protonated
Query graph of protonated carbonyl
165 compounds, 5 with experimental data

Nitrogen: amines and ammonium

amine I amine_primary
Query graph of amine I
13,857 compounds, 49 with experimental data
within: aliphatic amine
amine II amine_secondary
Query graph of amine II
14,306 compounds, 42 with experimental data
within: aliphatic amine
amine III amine_tertiary
Query graph of amine III
6,807 compounds, 50 with experimental data
within: aliphatic amine
aromatic amine I aromatic_amine_primary
Query graph of aromatic amine I
7,541 compounds, 39 with experimental data
within: aromatic amine
aromatic amine II aromatic_amine_secondary
Query graph of aromatic amine II
2,711 compounds, 14 with experimental data
within: aromatic amine
aromatic amine III aromatic_amine_tertiary
Query graph of aromatic amine III
688 compounds, 10 with experimental data
within: aromatic amine
alkylammonium 1° ammonium_primary
Query graph of alkylammonium 1°
8,781 compounds, 10 with experimental data
within: alkylammonium
alkylammonium 2° ammonium_secondary
Query graph of alkylammonium 2°
13,151 compounds, 12 with experimental data
within: alkylammonium
alkylammonium 3° ammonium_tertiary
Query graph of alkylammonium 3°
2,154 compounds, 5 with experimental data
within: alkylammonium
alkylammonium 4° ammonium_quaternary
Query graph of alkylammonium 4°
89 compounds, 1 with experimental data
within: alkylammonium
arylammonium 1° aromatic_ammonium_primary
Query graph of arylammonium 1°
1,020 compounds, 12 with experimental data
within: arylammonium (anilinium)
arylammonium 2° aromatic_ammonium_secondary
Query graph of arylammonium 2°
1,097 compounds, 2 with experimental data
within: arylammonium (anilinium)
arylammonium 3° aromatic_ammonium_tertiary
Query graph of arylammonium 3°
61 compounds, 3 with experimental data
within: arylammonium (anilinium)
arylammonium 4° aromatic_ammonium_quaternary
Query graph of arylammonium 4°
0 compounds
within: arylammonium (anilinium)

Nitrogen: acyl nitrogen

amide I amide_primary
Query graph of amide I
2,832 compounds, 5 with experimental data
within: amide (incl. lactam)
amide II amide_secondary
Query graph of amide II
3,594 compounds, 14 with experimental data
within: amide (incl. lactam)
amide III amide_tertiary
Query graph of amide III
2,400 compounds, 16 with experimental data
within: amide (incl. lactam)
lactam lactam
Query graph of lactam
8,602 compounds, 10 with experimental data
within: amide (incl. lactam)
imide imide
Query graph of imide
554 compounds, 9 with experimental data
amide/thioamide anion amide_anion
Query graph of amide/thioamide anion
4,792 compounds, 8 with experimental data
imide anion imide_anion
Query graph of imide anion
203 compounds, 1 with experimental data
urea urea
Query graph of urea
2,533 compounds, 14 with experimental data
carbamate carbamate
Query graph of carbamate
1,276 compounds, 9 with experimental data
carbamic acid carbamic_acid
Query graph of carbamic acid
25 compounds

Nitrogen: C=N family

amidine amidine
Query graph of amidine
9,409 compounds, 2 with experimental data
within: amidine or amidinium
amidinium amidinium
Query graph of amidinium
1,308 compounds
within: amidine or amidinium
guanidine guanidine
Query graph of guanidine
1,434 compounds, 3 with experimental data
within: guanidine or guanidinium
guanidinium guanidinium
Query graph of guanidinium
302 compounds
within: guanidine or guanidinium
imine imine
Query graph of imine
37,707 compounds
iminium iminium
Query graph of iminium
19,907 compounds, 4 with experimental data
oxime oxime
Query graph of oxime
3,706 compounds, 8 with experimental data
hydrazine hydrazine
Query graph of hydrazine
8,909 compounds, 7 with experimental data
hydrazone hydrazone
Query graph of hydrazone
3,127 compounds
azo azo
Query graph of azo
2,007 compounds, 1 with experimental data
azide azide
Query graph of azide
113 compounds, 11 with experimental data
diazo diazo
Query graph of diazo
440 compounds
triazene triazene
Query graph of triazene
357 compounds
nitrile nitrile
Query graph of nitrile
18,443 compounds, 49 with experimental data
nitrilium nitrilium
Query graph of nitrilium
2,178 compounds, 1 with experimental data
isocyanate isocyanate
Query graph of isocyanate
33 compounds, 2 with experimental data
isothiocyanate isothiocyanate
Query graph of isothiocyanate
86 compounds
thiocyanate thiocyanate
Query graph of thiocyanate
42 compounds

Nitrogen: N-O family

nitro nitro
Query graph of nitro
860 compounds, 46 with experimental data
nitrate nitrate
Query graph of nitrate
111 compounds, 16 with experimental data
nitroso nitroso
Query graph of nitroso
1,364 compounds
N-nitrosamine nitrosamine
Query graph of N-nitrosamine
377 compounds, 1 with experimental data
nitronate nitronate
Query graph of nitronate
88 compounds, 2 with experimental data
N-oxide n_oxide
Query graph of N-oxide
2,313 compounds
nitrone nitrone
Query graph of nitrone
593 compounds
hydroxylamine hydroxylamine
Query graph of hydroxylamine
3,097 compounds, 1 with experimental data
hydroxamic acid / N-alkoxy amide hydroxamic_acid
Query graph of hydroxamic acid / N-alkoxy amide
525 compounds, 5 with experimental data

Sulfur

thiol thiol
Query graph of thiol
5,428 compounds, 24 with experimental data
within: thiol or thiolate
thiolate thiolate
Query graph of thiolate
467 compounds, 5 with experimental data
within: thiol or thiolate
thioether thioether
Query graph of thioether
8,191 compounds, 31 with experimental data
disulfide disulfide
Query graph of disulfide
885 compounds, 4 with experimental data
thioester thioester
Query graph of thioester
141 compounds, 4 with experimental data
S-thiocarbamate thiocarbamate
Query graph of S-thiocarbamate
48 compounds, 2 with experimental data
thioamide thioamide
Query graph of thioamide
710 compounds, 2 with experimental data
thiourea thiourea
Query graph of thiourea
432 compounds, 1 with experimental data
thioketone / thioaldehyde thione
Query graph of thioketone / thioaldehyde
452 compounds
sulfoxide sulfoxide
Query graph of sulfoxide
351 compounds, 5 with experimental data
sulfinic acid sulfinic_acid
Query graph of sulfinic acid
16 compounds
within: sulfinic acid or sulfinate
sulfinate (anion) sulfinate
Query graph of sulfinate (anion)
0 compounds
within: sulfinic acid or sulfinate
sulfone sulfone
Query graph of sulfone
122 compounds, 5 with experimental data
sulfonamide sulfonamide
Query graph of sulfonamide
289 compounds, 7 with experimental data
within: sulfonamide (any form)
sulfonamide anion sulfonamide_anion
Query graph of sulfonamide anion
131 compounds, 2 with experimental data
within: sulfonamide (any form)
sulfonic acid sulfonic_acid
Query graph of sulfonic acid
127 compounds
within: sulfonic acid or sulfonate
sulfonate (anion) sulfonate
Query graph of sulfonate (anion)
40 compounds, 1 with experimental data
within: sulfonic acid or sulfonate
sulfonate ester sulfonate_ester
Query graph of sulfonate ester
51 compounds, 1 with experimental data
sulfonyl halide sulfonyl_halide
Query graph of sulfonyl halide
13 compounds, 1 with experimental data
sulfate diester sulfate_diester
Query graph of sulfate diester
3 compounds, 1 with experimental data
within: sulfate ester
sulfate monoester (acid) sulfate_monoester_acid
Query graph of sulfate monoester (acid)
92 compounds
within: sulfate monoester (acid or anion)
sulfate monoester (anion) sulfate_monoester_anion
Query graph of sulfate monoester (anion)
105 compounds
within: sulfate monoester (acid or anion)
sulfite sulfite
Query graph of sulfite
6 compounds, 3 with experimental data
sulfonium sulfonium
Query graph of sulfonium
6,752 compounds, 3 with experimental data

Phosphorus, silicon, boron, selenium

phosphate triester phosphate_triester
Query graph of phosphate triester
11 compounds, 8 with experimental data
within: phosphate ester
phosphate diester (acid) phosphate_diester_acid
Query graph of phosphate diester (acid)
8 compounds
within: phosphate diester (acid or anion)
phosphate diester (anion) phosphate_diester_anion
Query graph of phosphate diester (anion)
4 compounds
within: phosphate diester (acid or anion)
phosphate monoester (acid) phosphate_monoester_acid
Query graph of phosphate monoester (acid)
88 compounds
within: phosphate monoester (acid or anion)
phosphate monoester (anion) phosphate_monoester_anion
Query graph of phosphate monoester (anion)
16 compounds
within: phosphate monoester (acid or anion)
thiophosphate thiophosphate
Query graph of thiophosphate
54 compounds, 19 with experimental data
phosphonate diester phosphonate_diester
Query graph of phosphonate diester
28 compounds, 5 with experimental data
within: phosphonic acid, its anion or ester
phosphonate monoester (acid) phosphonate_monoester_acid
Query graph of phosphonate monoester (acid)
44 compounds
within: phosphonate monoester (acid or anion)
phosphonate monoester (anion) phosphonate_monoester_anion
Query graph of phosphonate monoester (anion)
4 compounds
within: phosphonate monoester (acid or anion)
phosphonic acid phosphonic_acid
Query graph of phosphonic acid
427 compounds
within: phosphonic acid or phosphonate anion
phosphonate (anion) phosphonate_anion
Query graph of phosphonate (anion)
113 compounds
within: phosphonic acid or phosphonate anion
phosphinic acid phosphinic_acid
Query graph of phosphinic acid
193 compounds
within: phosphinic acid or phosphinate
phosphinate (anion) phosphinate
Query graph of phosphinate (anion)
25 compounds
within: phosphinic acid or phosphinate
phosphine oxide phosphine_oxide
Query graph of phosphine oxide
13 compounds
phosphine phosphine
Query graph of phosphine
68 compounds, 1 with experimental data
silane silane
Query graph of silane
1 compounds, 1 with experimental data
within: organosilicon
siloxane siloxane
Query graph of siloxane
5 compounds, 5 with experimental data
within: organosilicon
silyl ether silyl_ether
Query graph of silyl ether
8 compounds, 8 with experimental data
within: organosilicon
boronic acid / ester boronic_acid
Query graph of boronic acid / ester
0 compounds
selenide selenide
Query graph of selenide
0 compounds

Aromatic rings

benzene ring phenyl
Query graph of benzene ring
6,873 compounds, 552 with experimental data
within: aromatic ring
pyridine pyridine
Query graph of pyridine
3,098 compounds, 52 with experimental data
within: azine (6-ring)
pyrimidine pyrimidine
Query graph of pyrimidine
3,032 compounds, 8 with experimental data
within: azine (6-ring)
pyridinone (2-/4-pyridone) pyridinone
Query graph of pyridinone (2-/4-pyridone)
376 compounds, 1 with experimental data
within: azine (6-ring), heteroaromatic lactam (pyridinone, pyrimidinone)
pyrimidinone (uracil/cytosine type) pyrimidinone
Query graph of pyrimidinone (uracil/cytosine type)
1,212 compounds, 13 with experimental data
within: azine (6-ring), heteroaromatic lactam (pyridinone, pyrimidinone)
pyrazine pyrazine
Query graph of pyrazine
922 compounds, 9 with experimental data
within: azine (6-ring)
pyridazine pyridazine
Query graph of pyridazine
732 compounds, 2 with experimental data
within: azine (6-ring)
1,3,5-triazine triazine
Query graph of 1,3,5-triazine
441 compounds, 9 with experimental data
within: azine (6-ring)
1,2,3-/1,2,4-triazine triazine_12x
Query graph of 1,2,3-/1,2,4-triazine
1,146 compounds, 1 with experimental data
within: azine (6-ring)
tetrazine tetrazine
Query graph of tetrazine
239 compounds
within: azine (6-ring)
pyrrole pyrrole
Query graph of pyrrole
3,175 compounds, 7 with experimental data
within: azole (5-ring)
indole indole
Query graph of indole
107 compounds, 3 with experimental data
within: azole (5-ring)
imidazole imidazole
Query graph of imidazole
5,292 compounds, 9 with experimental data
within: azole (5-ring)
pyrazole pyrazole
Query graph of pyrazole
3,638 compounds, 3 with experimental data
within: azole (5-ring)
1,2,3-triazole triazole_123
Query graph of 1,2,3-triazole
2,016 compounds, 1 with experimental data
within: triazole
1,2,4-triazole triazole_124
Query graph of 1,2,4-triazole
1,893 compounds, 1 with experimental data
within: triazole
tetrazole tetrazole
Query graph of tetrazole
765 compounds, 2 with experimental data
within: azole (5-ring)
furan furan
Query graph of furan
1,912 compounds, 14 with experimental data
within: heteroaromatic ring
thiophene thiophene
Query graph of thiophene
957 compounds, 31 with experimental data
within: heteroaromatic ring
oxazole oxazole
Query graph of oxazole
2,115 compounds, 5 with experimental data
within: azole (5-ring)
isoxazole isoxazole
Query graph of isoxazole
1,834 compounds, 3 with experimental data
within: azole (5-ring)
thiazole thiazole
Query graph of thiazole
1,455 compounds, 4 with experimental data
within: azole (5-ring)
isothiazole isothiazole
Query graph of isothiazole
197 compounds
within: azole (5-ring)
oxadiazole oxadiazole
Query graph of oxadiazole
2,351 compounds, 1 with experimental data
within: azole (5-ring)
thiadiazole thiadiazole
Query graph of thiadiazole
1,434 compounds
within: azole (5-ring)
purine purine
Query graph of purine
399 compounds, 4 with experimental data
within: heteroaromatic ring
pyranone (2-/4-pyrone, coumarin) pyranone
Query graph of pyranone (2-/4-pyrone, coumarin)
317 compounds
within: heteroaromatic ring
heteroaromatic ring (other) heteroaromatic_other
Query graph of heteroaromatic ring (other)
2,849 compounds
within: heteroaromatic ring

Charged centres

aromatic N cation (azinium) aromatic_n_cation
Query graph of aromatic N cation (azinium)
3,571 compounds, 10 with experimental data
aromatic N anion (azolide) aromatic_n_anion
Query graph of aromatic N anion (azolide)
1,228 compounds, 7 with experimental data
azanide (amine anion) azanide
Query graph of azanide (amine anion)
31,590 compounds, 8 with experimental data
nitrile anion (cyanocarbanion) nitrile_anion
Query graph of nitrile anion (cyanocarbanion)
124 compounds, 3 with experimental data
carbanion carbanion
Query graph of carbanion
8,993 compounds, 6 with experimental data
carbocation carbocation
Query graph of carbocation
2,112 compounds, 1 with experimental data

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